Secret Relationships
by Linds.C
Summary: When Jace confronts Alec about him sneaking out until morning everyday and asks him what 'girl' he is seeing, Alec is confused. He soon realizes what Jace meant and is torn between two choices. Alec is afraid that Jace won't accept him if he tells the truth, but if he doesn't their bond will suffer. Will he tell him, or risk the threat of breaking their bond? Contains Malec smut
1. Chapter 1

**This story is set in the books, where Alec had a secret relationship with Magnus. This is the first chapter I promise you there will be more. If you like it please like and comment. Feel free to send me requests for Shadowhunter Fanfics you want to read and I'll write them. I don't own the characters or setting in this story only the actual writing itself. I hope you like it; Enjoy!**

* * *

 **Alec's POV**

I quickly jumped in the shower after the hunt with Jace. We slaughtered a hoard of shax demons and I smell like ichor, sweat, and dirt so I decided to take a quick shower before sneaking out to go see Magnus. I threw on an old, faded black sweater with minimum holes and a pair of plain black jeans. I got past the training un-noticed until I heard an almost silent thud behind me.

"What's her name?" A familiar voice cooed behind me.

Jace.

I slowly turned to face him. He was just getting up from a kneeling position, the aftermath of jumping off something. I glanced up to see a window about 20 feet above him with a foot-deep ledge. He must have been spying on me. But how would he know that I was coming this way? Oh god, he's been watching me sneak out for a while.

"What?" I asked him, clearly confused. He just grinned and walked toward me, and I knew that there was no getting out of this now.

"C'mon, stop playing stupid. I'm your brother, you think I can't tell that you're in a relationship?" He said, staring me dead in the eyes. He knew about Magnus. How? Other than seeing me sneak out there was no other evidence that I was seeing Magnus. Was there?

"Relationship?" I decided to play dumb. But he wasn't buying it.

"Really Alec? Do you seriously think that I believe that? C'mon, I've seen you sneak out almost every night for the past month," He pushed. That was true but I could still through him off.

"I like to take late night walks," I replied with a shrug. I put one hand in my pocket and gave him a lazy grin.

"Oh really? So you've just been taking nightly walks that last until the early morning, and I suppose that the trees give you all the hickeys you constantly have on your neck?" I blushed a deep red. Of course, he sees the hickeys on my neck, cause nothing ever works out for me. At least he accepts me for being gay. "I have hard evidence, Alec," Jace continued, "so drop the stupid act and tell me what girl you're seeing." I might as well tell him, wait, what? Girl? he thinks I'm dating,

oh.

He thinks I've been seeing a girl. He doesn't know about Magnus. Jace thinks I'm straight. "Oh, um, I-I, it's just, I'm-" I stuttered as Jace raised his hand to shush me.

"Hey, you don't have to tell me her name now. Just, tell me sometime bro. I'm here for you if you want to tell me her name or not. I just have one question," He said, a little anxious.

"Okay, okay. Ask," I said nervously.

"OK, so, um...every time you came home early in the morning. Oh forget it, have you been screwing that girl you're seeing?" Jace said bluntly. I coughed a bit, then quickly scolded Jace.

"Jace!" I quietly yelled. He put his hands up in the air as surrender "okay, okay. I get it you're not that comfortable with talking about that stuff, yet. Sorry, just, you go see your girlfriend." He said and patted me on the shoulder. My smile faded and sadness clearly showed on my face.

"Uh yeah, I will. I gotta go, don't want to be late" I said quickly then left, not staying to hear his comment. So now he thinks I'm dating a girl. That's great. I can't tell him about Magnus, can I? I'm not sure. I'll talk to Magnus when I get to his loft. I do know one thing, though.

This is not going to end well.


	2. fights

**Magnus' POV**

I woke up to a calming warmth encasing my back. The gold silk sheets of my bed just covering us from the waist down. Last night, Alec arrived at 10 PM. I decided not to waste any time talking so I attacked his lips as soon as he stepped foot in the loft. By 11 we were both passed out in bed from our, _previous,_ actions. I could tell that something was troubling him but if it was really serious he would have brought it up already.

"I have to tell you something," a gentle quiet voice cooed right behind my neck. So it was important.

"go on," I whispered as I squeezed his arm gently in encouragement.

"okay, okay. Jace stopped me when I was sneaking out yesterday. He has been hiding up in the lofts watching me sneak out for a month now. He asked me what _girl_ I was seeing. He told me I didn't have to tell him about ' _her'_ today, that I can take my time. I considered telling him about you, but then I just agreed with him. And now he thinks I'm dating a girl, Magnus" he said my name as a whisper. He sounded so sad. I wasn't expecting this.

"Oh Alec," I said sweetly. I flipped over so that I could hug him against my chest. "Hey, everything is going to be fine. We will figure this out, okay? Now as much as I don't want you to go, it's 6 and you're parents will be looking for you soon. I can portal you to your room after you get dressed of course." I said with a sigh of disappointment. We both got up and put on clothes, I threw on a silk robe while Alec put on his jeans and a shirt.

"I'll see you tonight, and I'll make sure to tell you all the details," Alec said while giving me a quick goodbye kiss. I snapped up a portal and Alec walked through.

 **Jace's POV**

I rolled over in bed to shut off my alarm clock. I set it to 6 AM so I get up an hour before training starts, I want to talk to Izzy. I slowly got up and put a pair of jeans, a plain black shirt, and slipped on my shoes. I don't have to look great, most of the institute's occupants don't at this time of the morning. As I made my ways through the halls to Izzy's room I passed by other Shadowhunters, most of them going toward the training room, or leaving to follow up on a lead or mission. I even saw a team coming back from a hunt. Everyone at the institute was in between the ages 17 (new recruits) and 25, well except for Maryse and Robert who are rarely here; which leaves Alec as the acting head of the institute half the time.

I knocked on Izzy's door and opened it when I heard a "come in" from the other side. I walked in to find her standing in front of the mirror finishing the last of the two braids in her hair. She was dressed in black leggings, a sleeveless black turtleneck shirt, and sneakers that had 5-inch heels on the inside. When she tied the elastic onto the end of the braid she walked over to the vanity tidying things up

"What is it, Jace?" She asked while putting her stele into her pocket.

"Oh yes. Did you know that Alec is dating someone?" I questioned, and she immediately turned around to face me.

"Wait," she said with a look of confusion on her face, "So you know about Magnus?". Magnus? Why is she talking about Magnus?

"Why are you talking about Magnus? I'm talking about the fact that Alec has a girlfriend," I said with a furrowed brow. And Izzy returned the look.

"Wait, wait, wait. Girlfriend?" She asked. Why was she asking about that?

"Yes. Alec has a girlfriend, did you know that?" I repeated loud and clear.

"He does?! How did you find that out?" She demanded. Her face was full of shock. She looked kind of angry, surprised, and sad at the same time as I explained our encounter.

"I have to go, I'll see you later." Izzy quickly said then rushed out leaving me in her empty room.

 **Alec's POV**

I hopped in the shower as soon as I got to my room. By the time I had my pants and socks on Izzy burst into my room, not bothering to knock first. I turned around just in time to hear her asking me a billion questions.

"Izzy, slow down," I told her and she took a deep breath then started over again.

"Okay. Jace was just in my room asking me if I knew about "your girlfriend". So I said "so you know about Magnus?" but he completely ignored it, and wait what is that?" Izzy said brushing her fingertips over a hickey on my upper chest. I quickly put on a shirt.

"Izzy! Focus!" I reminded her.

"Sorry, okay. and he went back to you. What does he mean by a girlfriend? Omigod did you tell him you had a girlfriend Alec?" I looked away at the floor and she got the message. " I panicked Iz," I mumbled. I felt a hand rest on my arm,

"Alec, I support you 100% no matter who you are, or who you like. What makes you think that Jace won't? He's your parabatai, your brother and just like me he loves you too. Do you really think that that's going to change just because of your sexuality?" She said in a soothing voice.

"But what if you're wrong Iz. He's my parabatai, a part of me. I can't lose him," I confided in her.

"Well if he really is your parabatai, your brother, then he'll accept you for who you are. I'm not going to tell you how to come out, but I will tell you this; you should tell him, he'll be happy that you did," she finished. I saw her stand up on her tip-toes to give me a kiss on the cheek then she was gone. I have training with Jace in 10, but I decided to skip and get to work on the reports the Clave wants. As I made my way through the op-center towards Maryse's office.

About 20 minutes into my work as acting head Jace walked in. Great, just the person I wanted to avoid. He coughed dramatically to get my attention, and when I looked at him he looked confused.

"Training started 10 minutes ago. Why are you in here?" he questioned me, there was a slight anger in his tone.

"I'm the acting head of the institute, I should be in here. The question is why are you here? You have training now." I said like it was the most obvious thing in the world.

"Okay, what's wrong?" Jace questioned sitting down on a chair wary. I finally put my pen down and clasped my hands together looking straight at him.

"Nothing is wrong Jace. I just wanted to get a head start on all the reports the Clave wants," I put on my best fake normal face, but he still wasn't buying it. I returned my gaze to the paperwork and began scribbling on it again.

"Alec, come on. Look who you are talking to, buddy; you can tell me anything," Jace finished with a light chuckle. I slammed the pen down on the desk as he spoke the last part, making Jace flinch.

"Not this," I said through gritted teeth. Jace stood up and leaned on the desk.

"Alec, what's wrong with you? Is this about that girl you're seeing?" I stood up to face him, mirroring his exact position. I heard the slight crack the chair made when it hit the wall, sent there when I stood up so fast.

"You see that's exactly it Jace. But at the same time, it's not," I half-yelled. Jace furrowed his brow and looked at me with confusion. Before he could respond I continued,

"You should go. You have training and I have work," I said bitterly then sat down and continued to work. Jace, however, seemed to pretend he didn't hear me try to dismiss him and stayed.

"When you're ready to talk about it, I'm here." He said then walked out.


	3. The fighting never ends

**Magnus' POV**

"And that's what you missed," Alec finished his description of what happened at the institute. He explained his encounter with Izzy and the argument he had with Jace.

"Oh," I said. I was lying on the couch with Alec resting comfortably in between my legs, his back up against my chest. "So, what should I do?" He asked me, his voice sounding lost.

"I, I know you probably don't want to hear what I'm about to say, but I'm still going to say it. You've known Jace since he was 12, what makes you think that your sexuality will make him change his mind about those 10 years you known him?" I asked Alec in a tone that made it clear that the answer was oblivious. But this is Alec we're talking about so of course, you don't get any simple answer.

"Yeah, well I've known my mother longer, and if I came out to her she would disown me," Alec replied, and I know that he rolled his eyes even though I can't see his face.

"Well, Jace isn't homophobic," I retorted. Alec just sighed, and I waited patiently for a response knowing that it could take a while to get one. After a minute of him starting a sentence then finishing it before it got past 3 words, he finally spoke up.

"You don't know that. I, I want to tell him it's just, that I- he's my parabatai. He's a part of me, I can't lose him. I want to tell him, I do. I'm just afraid of what might happen,"

"If Jace is really your parabatai, if he _ever_ was your parabatai, then he wouldn't hate you because of your sexuality, Alexander. I'm not saying that you need to go to the institute and scream out that your gay to everyone, but you need to tell Jace. If he's your brother than he will love no less than he already does." I stated matter of factly. I expected an answer, not Alec standing up clearly annoyed and frustrated.

"No, okay? No. I-I can't. I just can't Magnus. I'm not going to risk losing a part of me. I need some sleep, I'm going to bed," he said in a slightly angry and hurt voice before stalking off to the bedroom. I waited half an hour before getting up and going to the bedroom. I quietly stripped down to my boxers and slipped under the covers, pressing my back up against his. I nuzzled my face into his neck and pressed my lips gently to the soft skin there.

"Are we okay?" I whispered in the dark silence, knowing that he was awake. My heart dropped after a minute of silence, but then I felt a warm hand press over one of mine, and a wave of relief washed over me.

"Always," a sure voice said. And with that word I let sleep carry me away.

* * *

"Alec it's been 6 days!" I yelled throwing my hands into the air. We were currently in the kitchen, standing on either side of the island arguing. Alec had just come back from the institute in a bad mood of course, from avoiding Jace. He just got a text from Jace and ignored it as if were nothing, and it set me off.

"Hmph, like I don't know that?" He yelled equally as angry.

"Okay. I don't want to fight, Alexander. We are capable of having a civilized conversation, right?" I sighed, trying to get my emotions back in check. Alec did the same and answered yes.

"Okay then. It has been 6 days since you last spoke to Jace. I thought you were going to talk to him?" I asked in an even voice. Alec huffed and then rolled his eyes.

"And who gave you that impression?" he asked in a sarcastic voice. He is making it so hard to be civilized right now, why can't he cut out the sarcasm for one second? He is always like this. I've tried talking about this more than once in the past 6 days but every time ending up the same way. It's impossible getting him to even consider telling Jace. I've even thought about telling him myself, but I stopped that thought as soon as it came knowing the I could never do that.

"Okay, I'm done suggesting. You will either promise to talk to Jace tomorrow, or you can leave now and not come back until you have. So which will it be?" I stated. I could feel guilt tug at my heart but I ignored it, knowing that this was the right thing to do. I stared him dead in the eyes and watched as a look mixed of hurt, anger, and confusion washed over his face.

"You're kicking _me_ out?" He asked me. I suddenly felt the guilt tug harder, but once again I pushed it down.

"No, I'm giving you 2 options. So what's your choice?" I said, trying to keep my voice steady. Alec's eyes looked a little glassy as he shook his head. Then he turned around and walked toward the door. It took every ounce of restraint in my body not to yell at him, to apologize and beg him to stay. As the loft door shut I pulled out my phone.

 _From: Magnus_

 _To: Isabelle_

 _I need your help with something_


	4. meet my boyfriend

**Alec's POV**

I was sitting in Maryse's office doing paperwork for the Clave when Izzy burst into the room. My head snapped up to attention and saw her looking rather shaken up.

"What's wrong," I demanded standing up walking towards her when she grabbed my arm and started pulling me out the door.

"Come on, hurry up Alec," she urged pulling me past other Shadowhunters staring at us weirdly as we rushed past them. She kept ignoring my questions, refusing to tell me what was going on. Finally, she let go of my arm when we reached the old meeting room. She walked in, gesturing for me to follow her in. As I did I followed her to behind a huge bookshelf, where I found nothing.

"what the hell, Izzy? why am I here?" I asked in an angry voice. She walked towards the door, me trailing behind by a few meters. When she turned around she had an apologetic look on her face.

"I'm sorry big brother, but this is for your own good," she said. I gave her a confused look, then Jace walked in. He looked at my angry expression, then Izzy's guilty one.

"Izzy," he began but she cut him off when she ran out the door and slammed it behind her, trapping me and Jace in the room.

I ran towards the door and tried to open it, only to find that it was locked. "Izzy!" I yelled.

"Neither of you is leaving that room until you tell him, Alec." she explained from the other side of the door, "I didn't want to do this, but if I don't you will never tell him. I'm sorry Alec, but you know it's true."

"Izzy! Izzy open the door!" I yelled pounding on the door.

"I'm sorry," Izzy said quietly before the sound of heels clicking on the floor grew quieter, and she was gone. I rammed into the door, once, twice, three times.

"Alec cut it out. It's not going to open, I'll call Clary," he said while reaching into his pocket. I turned away, and after seconds of silence, I turned around ready to question why it was taking so long when I saw Jace checking all of his pockets.

"My phone and stele are gone," he said confused. I just sighed in annoyance and reached to get my phone only to realize that it and my stele was absent as well. I was confused until I remembered "... _You either promise to talk to Jace tomorrow, or you can leave and not come back until you have..."_

 _"Magnus,_ " I cursed under my breath, but of course Jace heard it.

"Magnus?" He questioned, but I ignored it and went and sat down at the huge wooden table that use to be for meetings. I dropped my head into my hands and hunched over.

"What did Izzy mean by we can't leave until you tell me?" he probed on. "Fine," he huffed, "don't say anything. I don't care, but I will talk and you will listen. I don't know what I did, or how things got so awful between us, but I want it fixed before we leave this room. So you better hurry up and tell me what the hell is wrong-"

"me," I cut him off swiftly.

"What?"

"Me. I'm the problem. The reason why things are so messed up between us is that my feelings are in the way." I said still hiding my face in my hands.

"Alec is this is about the girl you're seeing, you can talk to me about anything you know. Especially girls, I have tons of experience in that area" he said with a smirk.

"I'm not dating a girl, Jace," I said, my tone sounding sad.

"Did you guys break up? Is this what you're so upset about?" he questioned, disbelief clear in his voice.

"No, my relationship is going great actually. Well at least it was until they sided with Izzy and helped steal our phones and steles," I mumbled. All of a sudden a loud smack sounded through the room and I turned to see Jace with his hand on the table, yelling.

"Damnit, Alec!" he shouted, "who is 'they'?" he demanded.

Once again I ran all the possible outcomes if I told Jace about Magnus. Only one out of many ends in him accepting me. I thought about lying, but my face gave it away and Jace told me not to lie. It's now or never, I guess. I took a deep breath then looked to Jace who had the same expression.

"I'm... their name... h-... um... I..." I stuttered, my breathing slowing increasing. Jace noticed and started to look worried, his angry and hard emotions slowly turning into supporting and patient ones.

"You can do it," he motivated quietly.

"Magnus," I blurted out, but quickly elaborated after seeing his confused face.

"Magnus Bane. I'm... I'm dating Magnus Bane," I finished quietly. Once he started to realize what that meant I looked away, not willing to see the look of disgust and anger that is probably taking over his expressions.

"So...that means... you're gay?" he asked. I flinched slightly at the word, knowing the shame and disgrace that came with it. I nodded, still not looking at Jace.

"This is what you've been upsetting you?" he asked. But instead of sounding disgusted and angry, he sounded...relieved and surprised. As if it was the least worst thing possible. I kept quiet, but that was enough of an answer.

"Alec, look at me," Jace pleaded. Time to face the music I guess. I looked up, to see Jace with a happy look on his face.

"I'm proud of you," he said. And the surprise and confusion clearly showed on my face.

"Look, Alec. I can obviously see how hard that was for you. And I'm proud of you. Okay, maybe you needed a little push from Izzy... and Magnus?" he asked, sounding unsure. I scratched the back of my neck awkwardly and replied.

"Well, ya. I mean he's been trying to convince me to tell you for weeks, saying that you would be supportive and all. Then yesterday I kinda yelled at him when he was trying to help and I got myself kicked out until I told you," I said awkwardly. Jace made a sound that sounded like a 'hmph'

"So, you were worried that I wouldn't accept you?" Jace asked, sounding a little hurt.

I looked away, not daring to see the hurt on his face. I get why he feels hurt and probably mad right now. Hey, I would be too. But I do have reasons, very, very, valid and appropriate reasons.

"Come on, Jace. You lived in Idris for 10 years. Probably the most homophobic place in the entire world. Then you came and lived with Maryse and Robert. I had very good reasons to be worried that you wouldn't accept me." I stated very matter of factly. Jace nodded in agreement.

"Well, just so I'm clear, I accept and support you, Alec. You are my brother, and nothing will change that. Especially not your sexuality. I love you, buddy." Jace said outstretching his hand, waiting for me to initiate the. I clasped his hand in my own and pulled him into a brotherly hug.

"I love you too, brother." I murmured. When we pulled apart Jace had that same old mischevious and smug grin on his face. The one that told me he was up to something.

"So, Magnus Bane, huh. How'd that happen?" he asked smugly. I blushed darkly, thinking of the first times I saw Magnus. The way he kissed me when I asked him out. That was a surprise. My first kiss, with a man so handsome and kind. Then how I kissed him, then fell down the stairs after.

"Oh, um... I-I actually asked him out. After he saved my life... and um, ya. We went out on a date, kissed twice actually." I said awkwardly while blushing. Jace smirked.

"Wow, I didn't know you were so bold, Alec." He cooed and we both laughed. Just then the door to the room creaked open. Jace slung his arm around my shoulders, proving it challenging but we made it work. We walked out to find our steles and phones in the middle of the dead corridor. After we picked them I went to messages, about to text him, but then thought better of it.

"Hey, um I need to go talk to Magnus..." I started, "would you, um, like to come and meet him? As my boyfriend, I mean," I finished awkwardly. Jace smiled then nodded.

"I've been waiting my whole life for you to introduce me to your...someone who you were seeing. Seems the day has finally come where I get to meet you're first ever partner," he stated.

"Yeah," I said in a breath, " I guess so"

And with that, we walked out of the institute and started towards Magnus' loft.


End file.
